I mean I think bees are harmed in the production of honey, it’s just that most people don’t care about bee welfare. Commercially they’re bred by crushing the male to extract semen, and any operation above hobby scale will clip the wings of the queen so that the hive can’t escape.

Then you necessarily need to replace their ideal food source with something that is nutritionally much worse for them (basically sugar water), and then hope that they survive on that long enough to make more honey for us to take.